diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..3966313 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,19 @@ +include *.rst +include aldy/resources/*.rst +include aldy/resources/genes/*.yml +include aldy/resources/genes/pharmacoscan/*.yml +include aldy/resources/profiles/*.yml +include aldy/tests/resources/*.json +include aldy/tests/resources/*.bam +include aldy/tests/resources/*.bai +include aldy/tests/resources/*.expected +include aldy/tests/resources/*.yml +include aldy/tests/resources/*.profile +include aldy/tests/resources/*.hg38 +include aldy/tests/resources/*.vcf +include aldy/tests/resources/*.gz +include aldy/tests/resources/*.tbi +include aldy/indelpost/*.pyx +include aldy/indelpost/*.pxd +include aldy/indelpost/ssw.h +include aldy/indelpost/sse2neon.h diff --git a/setup.py b/setup.py index 3f1c4f8..464d2a2 100644 --- a/setup.py +++ b/setup.py @@ -96,47 +96,7 @@ ], entry_points={"console_scripts": ["aldy = aldy.__main__:console"]}, packages=find_packages(), - package_data={ - "aldy.resources": ["*.rst", "aldy/resources/*.rst"], - "aldy.resources.genes": [ - "*.yml", - "aldy/resources/genes/*.yml", - "aldy/resources/genes/pharmacoscan/*.yml", - ], - "aldy.resources.profiles": ["*.yml", "aldy/resources/profiles/*.yml"], - "aldy.tests.resources": [ - "*.json", - "aldy/tests/resources/*.json", - "*.bai", - "aldy/tests/resources/*.bai", - "*.bam", - "aldy/tests/resources/*.bam", - "*.expected", - "aldy/tests/resources/*.expected", - "*.yml", - "aldy/tests/resources/*.yml", - "aldy/tests/resources/pharmacoscan/*.yml", - "*.profile", - "aldy/tests/resources/*.profile", - "*.hg38", - "aldy/tests/resources/*.hg38", - "*.vcf", - "aldy/tests/resources/*.vcf", - "*.gz", - "aldy/tests/resources/*.gz", - "*.tbi", - "aldy/tests/resources/*.tbi", - ], - "aldy.indelpost": [ - "*.pyx", - "aldy/indelpost/*.pyx", - "*.pxd", - "aldy/indelpost/*.pxd", - "*.h", - "aldy/indelpost/ssw.h", - "aldy/indelpost/sse2neon.h", - ], - }, + include_package_data=True, cmdclass={"build_ext": build_ext}, ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}), test_suite="pytest-runner",